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» Computing with Evolving Proteins
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IPPS
2007
IEEE
16 years 1 months ago
High Performance Database Searching with HMMer on FPGAs
1 Profile Hidden Markov Models (profile HMMs) are used as a popular bioinformatics tool for sensitive database searching, e.g. a set of not annotated protein sequences is compared...
Timothy F. Oliver, Leow Yuan Yeow, Bertil Schmidt
ALMOB
2007
155views more  ALMOB 2007»
15 years 6 months ago
Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid rep
Background: Some amino acid residues functionally interact with each other. This interaction will result in an evolutionary co-variation between these residues – coevolution. Ou...
Rodrigo Gouveia-Oliveira, Anders Gorm Pedersen
BMCBI
2008
187views more  BMCBI 2008»
15 years 6 months ago
PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes
Background: The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved...
Christine Fong, Laurence Rohmer, Matthew Radey, Mi...
BMCBI
2007
140views more  BMCBI 2007»
15 years 6 months ago
Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on
Background: A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes...
Yung-Keun Kwon, Sun Shim Choi, Kwang-Hyun Cho
BMCBI
2006
137views more  BMCBI 2006»
15 years 6 months ago
Sigma: multiple alignment of weakly-conserved non-coding DNA sequence
Background: Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch...
Rahul Siddharthan